In this Phase I application IsoPlexis proposes to deliver a novel method for targeted profiling of both the transcriptome and secretome from an array of 1000+ single central and peripheral immune cells. Specifically, we will deliver a single-cell, mRNA and secreted protein capture assay with proven sensitivity for detecting the most important predictive biomarkers for neurodegenerative diseases. There is growing evidence of the immune system acting in a functional or dysfunctional manner in neurodegenerative diseases and their cellularly heterogeneous microenvironments taken on therapeutic significance. The function of microglia has been implicated in Alzheimer's Disease, Frontotemporal Dementia, ALS, and MS among many more. To best utilize the growing scientific understanding of immune response to genetic/epigenetic factors contributing to neurodegenerative disease, an integrated tool is needed to (i) make highly multiplexed, quantitative measurements thousands of single cells (ii) while being able to gather both precise proteomic and transcriptomic data from the same cell (iii) with fully automated, high throughput. We at IsoPlexis propose to develop an integrated and comprehensive platform to capture and characterize secreted protein response and the mRNA transcriptome, for downstream RNA-Seq, in a cell-specific manner, with minimal user variability. Aim 1. Develop an SCBC injection flow cell for the dual capture of secreted proteins and subsequent cell lysis for transcriptome on-device. Aim 2. Demonstrate the ability to monitor transcriptome and multiplexed secreted protein biomarkers from 1000+ single microglia and monocytes from a 10+ neurodegenerative disease mouse study and monocytes from 5 Alzheimer's Disease and 5 Frontotemporal Dementia patient samples in collaboration with UCI and UCSF. Transition to Phase II: (i) With the fully functional and validated flow cell, we will seek out 2+ clinical/preclinical collaborations with institutes currently researching genetic correlations and immune system involvement in neurodegenerative diseases. (ii) We will demonstrate the mRNA/secretion assay on a fully-automated SCBC instrument, the IsoLight, from cell isolation all the way to the final analysis improving throughput and reducing variability.